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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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2
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Mao H, Cao Y, Zou Z, Xia J, Zhao J. An enzyme-powered microRNA discriminator for the subtype-specific diagnosis of breast cancer. Chem Sci 2023; 14:2097-2106. [PMID: 36845930 PMCID: PMC9944337 DOI: 10.1039/d3sc00090g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Breast cancer, a disease with highly heterogeneous features, is the most common malignancy diagnosed in people worldwide. Early diagnosis of breast cancer is crucial for improving its cure rate, and accurate classification of the subtype-specific features is essential to precisely treat the disease. An enzyme-powered microRNA (miRNA, RNA = ribonucleic acid) discriminator was developed to selectively distinguish breast cancer cells from normal cells and further identify subtype-specific features. Specifically, miR-21 was used as a universal biomarker to discriminate between breast cancer cells and normal cells, and miR-210 was used to identify triple-negative subtype features. The experimental results demonstrated that the enzyme-powered miRNA discriminator displayed low limits of detection at fM levels for both miR-21 and miR-210. Moreover, the miRNA discriminator enabled the discrimination and quantitative determination of breast cancer cells derived from different subtypes based on their miR-21 levels, and the further identification of the triple-negative subtype in combination with the miR-210 levels. Therefore, it is hoped that this study will provide insight into subtype-specific miRNA profiling, which may have potential use in the clinical management of breast tumours based on their subtype characteristics.
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Affiliation(s)
- Huiru Mao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University Shanghai 200444 P. R. China
| | - Ya Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing UniversityNanjing 210023P. R. China
| | - Zihan Zou
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University Shanghai 200444 P. R. China
| | - Jianan Xia
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University Shanghai 200444 P. R. China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University Shanghai 200444 P. R. China
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3
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Chovelon B, Peyrin E, Ragot M, Salem N, Nguyen TG, Auvray B, Henry M, Petrillo MA, Fiore E, Bessy Q, Faure P, Ravelet C. Nile blue as reporter dye in salt aggregation based-colorimetric aptasensors for peptide, small molecule and metal ion detection. Anal Chim Acta 2023; 1243:340840. [PMID: 36697182 DOI: 10.1016/j.aca.2023.340840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/21/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Herein, we report a novel approach for the design of a colorimetric aptasensor, relying on a Dye Salt Aggregation-based Colorimetric Oligonucleotide assay (DYSACO assay). This method is based on the use of an intercalating agent, Nile Blue (NB), whose aggregation capacities (and thus modification of its absorption spectrum) are drastically amplified by adding salts to the working solution. The presence of an aptamer could protect NB from such aggregation process due to its intercalation into double-stranded DNA and/or interaction with nucleobases. In response to the addition of the specific ligand, the competition between NB and the target for binding to the aptamer occurs, resulting in an increase in the dye salt aggregation and then in the blue-to-blank color change of the solution. The proof-of-principle was demonstrated by employing the anti-l-tyrosinamide aptamer and the assay was successfully applied to the trace enantiomer detection, allowing the detection of an enantiomeric impurity down to approximately 2% in a non-racemic sample. Through a reversed mechanism based on the increased capture of NB by DNA upon analyte binding, the sensing platform was further demonstrated for the Hg(II) detection. Water samples of different origin were spiked with Hg(II) analyte at final range concentrations comprised between (0.5-15 μM). An excellent overall recovery of 122 ± 14%; 105 ± 14%; 99 ± 9%; was respectively obtained from river, tap and mineral water, suggesting that the sensor can be used under real sample conditions. The assay was also shown to work for sensing the ochratoxin A and d-arginine vasopressin compounds, revealing its simplicity and generalizability potentialities.
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Affiliation(s)
- Benoît Chovelon
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
| | - Mailys Ragot
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Nassim Salem
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Truong Giang Nguyen
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Benjamin Auvray
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mickael Henry
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mel-Alexandre Petrillo
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Quentin Bessy
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Patrice Faure
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
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4
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Wallin J, Lönnberg T. Improved Synthesis Strategy for N‐Methoxy‐1,3‐Oxazinane Nucleic Acids (MOANAs). European J Org Chem 2022. [DOI: 10.1002/ejoc.202200538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Josefiina Wallin
- University of Turku: Turun Yliopisto Department of Chemistry FINLAND
| | - Tuomas Lönnberg
- University of Turku Dept. of Chemistry Vatselankatu 2 20014 Turku FINLAND
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5
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Afari MNK, Virta P, Lönnberg T. N-Methoxy-1,3-oxazinane nucleic acids (MOANAs) - a configurationally flexible backbone modification allows post-synthetic incorporation of base moieties. Org Biomol Chem 2022; 20:3480-3485. [PMID: 35388869 DOI: 10.1039/d2ob00465h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
(2R,3S)-4-(Methoxyamino)butane-1,2,3-triol was converted into a protected phosphoramidite building block and incorporated into the middle of a short DNA oligonucleotide. O1 and O3 of the (2R,3S)-4-(methoxyamino)butane-1,2,3-triol were engaged in phosphodiester linkages, leaving O2 and the methoxyamino function available to form an N-methoxy-1,3-oxazinane ring through reaction with an aldehyde. In modified oligonucleotides thus obtained, the oxazinane ring formally replaces the furanose ring and the aldehyde, the base moiety of natural nucleosides. The feasibility of synthesizing base-modified oligonucleotides by this approach was demonstrated with several aromatic and aliphatic aldehydes featuring various functional groups.
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Affiliation(s)
- Mark N K Afari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Pasi Virta
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Zhang A, Kondhare D, Leonard P, Seela F. 5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts. Chemistry 2021; 27:7453-7466. [PMID: 33443814 PMCID: PMC8251886 DOI: 10.1002/chem.202005199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/19/2022]
Abstract
The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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8
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Antiviral activity spectrum of phenoxazine nucleoside derivatives. Antiviral Res 2019; 163:117-124. [PMID: 30684562 DOI: 10.1016/j.antiviral.2019.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/13/2022]
Abstract
The phenoxazine scaffold is widely used to stabilize nucleic acid duplexes, as a part of fluorescent probes for the study of nucleic acid structure, recognition, and metabolism, etc. Here we present the synthesis of phenoxazine-based nucleoside derivatives and their antiviral activity against a panel of structurally diverse viruses: enveloped DNA herpesviruses varicella zoster virus (VZV) and human cytomegalovirus, enveloped RNA tick-borne encephalitis virus (TBEV), and non-enveloped RNA enteroviruses. Studied compounds were effective against DNA and RNA viruses reproduction in cell culture. 3-(2'-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenoxazine proved to be a potent inhibitor of VZV replication with superior activity against wild type than thymidine kinase deficient strains (EC50 0.06 and 10 μM, respectively). This compound did not show cytotoxicity on all the studied cell lines. Several compounds showed promising activity against TBEV (EC50 0.35-0.91 μM), but the activity was accompanied by pronounced cytotoxicity. These compounds may be considered as a good starting point for further structure optimization as antiherpesviral or antiflaviviral compounds.
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9
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Brissos RF, Clavero P, Gallen A, Grabulosa A, Barrios LA, Caballero AB, Korrodi-Gregório L, Pérez-Tomás R, Muller G, Soto-Cerrato V, Gamez P. Highly Cytotoxic Ruthenium(II)-Arene Complexes from Bulky 1-Pyrenylphosphane Ligands. Inorg Chem 2018; 57:14786-14797. [DOI: 10.1021/acs.inorgchem.8b02541] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rosa F. Brissos
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Pau Clavero
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Albert Gallen
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Arnald Grabulosa
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | - Ana B. Caballero
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Luís Korrodi-Gregório
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Campus Bellvitge, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain
| | - Ricardo Pérez-Tomás
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Campus Bellvitge, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain
| | - Guillermo Muller
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Vanessa Soto-Cerrato
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Campus Bellvitge, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain
| | - Patrick Gamez
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
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10
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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11
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Wang Z, Zhao J, Li Z, Bao J, Dai Z. Sequence and Structure Dual-Dependent Interaction between Small Molecules and DNA for the Detection of Residual Silver Ions in As-Prepared Silver Nanomaterials. Anal Chem 2017; 89:6815-6820. [DOI: 10.1021/acs.analchem.7b01238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhaoyin Wang
- Jiangsu Collaborative Innovation
Center of Biomedical Functional Materials and Jiangsu Key Laboratory
of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Jian Zhao
- Jiangsu Collaborative Innovation
Center of Biomedical Functional Materials and Jiangsu Key Laboratory
of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Zijun Li
- Jiangsu Collaborative Innovation
Center of Biomedical Functional Materials and Jiangsu Key Laboratory
of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Jianchun Bao
- Jiangsu Collaborative Innovation
Center of Biomedical Functional Materials and Jiangsu Key Laboratory
of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Zhihui Dai
- Jiangsu Collaborative Innovation
Center of Biomedical Functional Materials and Jiangsu Key Laboratory
of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
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12
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Radhika R, Shankar R, Vijayakumar S, Kolandaivel P. Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:1369-1401. [PMID: 28436311 DOI: 10.1080/07391102.2017.1323013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇2ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.
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Affiliation(s)
- R Radhika
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - R Shankar
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - S Vijayakumar
- b Department of Medical Physics , Bharathiar University , Coimbatore , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore , India
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13
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Lou C, Samuelsen SV, Christensen NJ, Vester B, Wengel J. Oligonucleotides Containing Aminated 2'-Amino-LNA Nucleotides: Synthesis and Strong Binding to Complementary DNA and RNA. Bioconjug Chem 2017; 28:1214-1220. [PMID: 28332825 DOI: 10.1021/acs.bioconjchem.7b00061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.
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Affiliation(s)
| | | | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg 1871, Denmark
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14
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Balijapalli U, Udayadasan S, Panyam Muralidharan V, Sukumarapillai DK, Shanmugam E, Paduthapillai Gopal A, S Rathore R, Kulathu Iyer S. An insight into the photophysical properties of amide hydrogen bonded N-(benzo[d]thiazol-2-yl) acetamide crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:572-577. [PMID: 27776311 DOI: 10.1016/j.saa.2016.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 10/11/2016] [Indexed: 06/06/2023]
Abstract
Three distinct, hydrogen bond associated N-(benzo[d]thiazol-2-yl) acetamides were synthesized by refluxing benzothiazoles with acetic acid. The nature of the assemblies was characteristic to the substituent in the benzothiazole moiety. In N-(benzo[d]thiazol-2-yl)acetamide, water acts as a bridge for forming three hydrogen bonds, as an acceptor to amide NH, and donors to carbonyl of amide and thiazole nitrogen assembles of three different N-(benzo[d]thiazol-2-yl)acetamide molecules. The N-(6-methylbenzo[d]thiazol-2-yl)acetamide formed a (amide) N-H…N (thiazole) bonded R22(8) molecular dimers by two homo-intermolecular hydrogen bonding interactions. N-(6-methoxybenzo[d]thiazol-2-yl)acetamide formed (amide)N-H…O (acid) & (acid)O-H…N (thiazole) interactions with the acetic acid, forming a R22(8) hydrogen-bonded ring by two hetero-intermolecular hydrogen bonding interactions.
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Affiliation(s)
- Umamahesh Balijapalli
- School of Advanced Sciences, Vellore Institute of Technology University, Vellore, India
| | - Sathiskumar Udayadasan
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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15
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Akula HK, Kokatla H, Andrei G, Snoeck R, Schols D, Balzarini J, Yang L, Lakshman MK. Facile functionalization at the C4 position of pyrimidine nucleosides via amide group activation with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and biological evaluations of the products. Org Biomol Chem 2017; 15:1130-1139. [PMID: 28054092 PMCID: PMC5367150 DOI: 10.1039/c6ob02334g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of O-t-butyldimethylsilyl-protected thymidine, 2'-deoxyuridine, and 3'-azidothymidine (AZT) with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) leads to activation of the C4 amide carbonyl by formation of putative O4-(benzotriazol-1-yl) derivatives. Subsequent substitution with alkyl and aryl amines, thiols, and alcohols leads to facile functionalization at this position. Reactions with amines and thiols were conducted either as a two-step, one-pot transformation, or as a one-step conversion. Reactions with alcohols were conducted as two-step, one-pot transformations. In the course of these investigations, the formation of 1-(4-pyrimidinyl)-1H-benzotriazole-3-oxide derivatives from the pyrimidine nucleosides was identified. However, these too underwent conversion to the desired products. Products obtained from AZT were converted to the 3'-amino derivatives by catalytic reduction. All products were assayed for their abilities to inhibit cancer cell proliferation and for antiviral activities. Many were seen to be active against HIV-1 and HIV-2, and one was active against herpes simplex virus-1 (HSV-1).
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Affiliation(s)
- Hari K Akula
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Hariprasad Kokatla
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Jan Balzarini
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Lijia Yang
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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16
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Zhao HQ, Yang SP, Ding NN, Qin L, Qiu GH, Chen JX, Zhang WH, Chen WH, Hor TSA. A zwitterionic 1D/2D polymer co-crystal and its polymorphic sub-components: a highly selective sensing platform for HIV ds-DNA sequences. Dalton Trans 2016; 45:5092-100. [DOI: 10.1039/c5dt04410c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (2, 1D chain), [Cu(dcbb)2]n (3, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n (4) have been prepared from the reaction of [Na(dcbb)(H2O)]n (1) with Cu(NO3)2·3H2O at different temperatures.
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Affiliation(s)
- Hai-Qing Zhao
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Shui-Ping Yang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ni-Ni Ding
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Liang Qin
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Gui-Hua Qiu
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - T. S. Andy Hor
- Institute of Materials Research and Engineering (IMRE)
- A*STAR
- Singapore
- Department of Chemistry
- National University of Singapore
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17
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Yang SP, Chen SR, Liu SW, Tang XY, Qin L, Qiu GH, Chen JX, Chen WH. Platforms Formed from a Three-Dimensional Cu-Based Zwitterionic Metal-Organic Framework and Probe ss-DNA: Selective Fluorescent Biosensors for Human Immunodeficiency Virus 1 ds-DNA and Sudan Virus RNA Sequences. Anal Chem 2015; 87:12206-14. [PMID: 26619043 DOI: 10.1021/acs.analchem.5b03084] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We herein report a water-stable three-dimensional Cu-based metal-organic framework (MOF) 1 supported by a tritopic quaternized carboxylate and 4,4'-dipyridyl sulfide as an ancillary ligand. This MOF exhibits unique pore shapes with aromatic rings, positively charged pyridinium and unsaturated Cu(II) cation centers, free carboxylates, tessellating H2O, and coordinating SO4(2-) on the pore surface. Compound 1 can interact with two carboxyfluorescein (FAM)-labeled single-stranded DNA sequences (probe ss-DNA, delineated as P-DNA) through electrostatic, π-stacking, and/or hydrogen-bonding interactions to form two P-DNA@1 systems, and thus quench the fluorescence of FAM via a photoinduced electron-transfer process. These P-DNA@1 systems can be used as effective fluorescent sensors for human immunodeficiency virus 1 double-stranded DNA and Sudan virus RNA sequences, respectively, with detection limits of 196 and 73 pM, respectively.
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Affiliation(s)
- Shui-Ping Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Shao-Rui Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Shu-Wen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Xiao-Yan Tang
- Department of Chemistry and Materials Engineering, Jiangsu Key Laboratory of Advanced Functional Materials, Changshu Institute of Technology , Changshu 215500, Jiangsu P. R. China
| | - Liang Qin
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Gui-Hua Qiu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, P. R. China
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18
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Lou C, Vester B, Wengel J. Oligonucleotides containing a piperazino-modified 2'-amino-LNA monomer exhibit very high duplex stability and remarkable nuclease resistance. Chem Commun (Camb) 2015; 51:4024-7. [PMID: 25659978 DOI: 10.1039/c5cc00322a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Incorporation of a piperazino-modified 2'-amino-LNA monomer (PipLNA-T) into oligonucleotides conferred very high affinity and base-pairing selectivity towards complementary DNA and RNA strands. Furthermore, one PipLNA-T modification provided a robust nuclease resistance that safeguarded three neighbouring natural nucleosides from 3'-exonucleolytic degradation. These favourable properties render PipLNA-T a promising oligonucleotide modification for various biological applications.
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Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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19
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Bartolami E, Gilles A, Dumy P, Ulrich S. Synthesis of α-PNA containing a functionalized triazine as nucleobase analogue. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Paolantoni D, Cantel S, Dumy P, Ulrich S. A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies. Int J Mol Sci 2015; 16:3609-25. [PMID: 25667976 PMCID: PMC4346916 DOI: 10.3390/ijms16023609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
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Affiliation(s)
- Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
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21
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Chambers MB, Wang X, Elgrishi N, Hendon CH, Walsh A, Bonnefoy J, Canivet J, Quadrelli EA, Farrusseng D, Mellot-Draznieks C, Fontecave M. Photocatalytic carbon dioxide reduction with rhodium-based catalysts in solution and heterogenized within metal-organic frameworks. CHEMSUSCHEM 2015; 8:603-608. [PMID: 25613479 DOI: 10.1002/cssc.201403345] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 06/04/2023]
Abstract
The first photosensitization of a rhodium-based catalytic system for CO2 reduction is reported, with formate as the sole carbon-containing product. Formate has wide industrial applications and is seen as valuable within fuel cell technologies as well as an interesting H2 -storage compound. Heterogenization of molecular rhodium catalysts is accomplished via the synthesis, post-synthetic linker exchange, and characterization of a new metal-organic framework (MOF) Cp*Rh@UiO-67. While the catalytic activities of the homogeneous and heterogeneous systems are found to be comparable, the MOF-based system is more stable and selective. Furthermore it can be recycled without loss of activity. For formate production, an optimal catalyst loading of ∼10 % molar Rh incorporation is determined. Increased incorporation of rhodium catalyst favors thermal decomposition of formate into H2 . There is no precedent for a MOF catalyzing the latter reaction so far.
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Affiliation(s)
- Matthew B Chambers
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, UPMC Univ Paris 06, Collège de France, 11 Marcelin Berthelot, 75231 Paris Cedex 05, France, Fax: +33 1 44271356 ; Tel: +33 1 44271360
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